Legendary War
by SuperMigo
Summary: An epic battle is brewing in the world of Pokemon and Mewtwo has taken it upon himself become the catalyst. With the help of Deoxys, he's shaping up a war that's sure to change the entire universe, however his murky intentions might prove to be fatal.
1. Black Market

**Chapter 1: Black Market**

About twenty hunters stand over the corpse of Deoxys. The sapphire crystal in its chest quickly dimmed into a deathly gray. As the hunters celebrate in a forest on the Western part of Sinnoh, there begins chatter of the profit that prompted the capture of the alien pokemon's body.

One of the troops asked the commander "How much was the lab offering for this warrant?"

Commander Bradfield answered him with the best of his ability. "There's no telling. I would say fifty million dollars, but even that's lowballing it. How much would you pay to be able to research something of only two on the planet?"

"There's two of these things?" The troop responded.

"Yep. This is one of two. Two pokemon that might not even native to this planet. We could've got a bigger price for him if we kept him alive, but we couldn't risk it. Five months ago another squad of hunters contracted by a lab in Kanto tried to get a hold of it. Absolute massacre. Thirty something bodies because of an underestimation." The commander explained.

The hunters were under contract for the Canalave City Weapons and Technology Lab. What used to be a legitimate research company ten years ago was now a vicious underground business that made profit from making weapons. These weapons were crafted from the cruel experimentation of pokemon captured by force. Capturing these pokemon by way of pokeballs was not an option. A modern law enacted by the government made it so that as soon as a pokemon is captured by pokeball, it is registered and tracked by federal anti-abuse agencies. Pokemon that are abused or tortured can be easily traced back to the owner if caught by pokeball, leading to felony charges. But underground labs found a way around the law by using pure force to get the job done. The underground weapons market was growing bigger every day.

"Did you hear that?" One of the troops said. Suddenly, the whole squadron became dead silent. There was no noise except the trees rustling, the wind blowing, and slight chirps by irrelevant bugs in the area. But there was an eerie feeling. The feeling that they weren't alone.

Bradfield pressed his earpiece. "Lookout, do you see anything?"

There was no answer.

"Lookout do you read, do you have eyes on anything in the area."

Again, no answer. The commander grabbed his binoculars to look at the sniper he had on a hilltop to watch out for the squad. As he zoomed in his binoculars, he was shocked to see that his sniper was dead. Gasping in fear, the Bradfield dropped his binoculars.

He started to yell at the top of his lungs "Hostile in the area, everybody…"

He didn't even finish his command. As he turned around, his whole squad was dead. Eyes rolled in the back of their heads. Panicking, the commander grabbed his assault rifle, frantically searching for the cause of his deceased army. His heart pounded as if it was beating out of his chest, and then he froze. Not only could he not move, but he didn't have the will to even speak. As sweat starts dripping down his forehead, he feels himself getting launched into a tree by a powerful force. He was stuck. The only movement this strange force was allowing him to do was move his head. And as he looked down to his rifle that he dropped on the ground. There, he saw something that he was never expecting to see.

"Mewtwo?" Bradfield exclaimed. There stood the original legendary pokémon himself, eyes glowing with purple rage.

"What do you want with me?" Bradfield cried.

"The people that you're employed with. Their purpose ends today."

Mewtwo read Bradfield's mind and shut down his brain, killing him instantly.

Six hours later at Canalave City Weapons and Technology Lab a group of armed men came through the metal doors. On the outside, the lab fronted as a simple warehouse with nothing of note happening on the inside. But on the inside, there was a highly sophisticated lab equipped with some of the most high-tech research equipment that most of the labs in the modern world couldn't afford. Also, somewhere in this lab there was a floor entrance to an elevator in hiding. This elevator led to a bank of different pokemon being tested and tortured. Hallways packed with Crowbats and Koffings used to make weapons that world has never seen before. Today, the lab just got their most valuable Pokemon yet.

As about thirty or so men walked in, there was the other Deoxys, wrapped in plasma tie that was somehow keeping its powers at bay. This one had a green crystal in it's chest and it was still alive, even though it was damaged and utterly defeated. The commander of this group walked up to the head lab technician, Professor Mackey.

"We lost three men in the field. But take a look. Alive and at mercy," Commander Greg said to technician, as he poked Deoxys with the end of his rifle.

Professor Mackey observed Deoxys. He walked around the captured Pokemon a couple of times, and everywhere he stepped Deoxys's eyes following. He started touching Deoxys, almost in disbelief that it was alive and in his presence. The professor had more than a few questions on his mind.

"Well done Greg, you'll be compensated for your lost men and of course your capture once we start getting it through confinement procedures. Have you heard from the other unit?"

"No feedback." Mackey put bluntly. "We've tried contacting them for two hours straight. Not a word from anybody."

"We lost contact with them a couple of hours ago. Jesus, what happened? The last info I got from them is that they the had to kill the other Deoxys and were on the way back with the corpse." Mackey said.

"Damn. We might have to pull a recon mission to find out what happened to those idiots." Greg said.

Immediately after, there was a loud explosion from above. All the scientists and soldiers immediately went on alert. Sirens and red lights started going off in the lab, signaling an unusual emergency. A loud screeching sound coming from the elevator shaft had everybody covering their ears. When the screeching stopped, all the armed squadron members pointed their automatic rifles to the metal doors with their fingers firmly on the triggers. There was a wait that seemed like it was lasting forever. Who came to ruin the party?

The elevator doors split open rapidly. It was Mewtwo.

Without hesitation everyone opened fired on Mewtwo. A hail of bullets headed for the Pokemon. But then, they all stopped abruptly in midair before they could even reach Mewtwo. What was supposed to kill Mewtwo ended up being a wall up bullets being stopped telekinetically before reaching him. When the squad started hearing empty clips, there was a collective terror in the underground lab.

"You've all been profiting off the lives of Pokemon for your own sadistic reasons. And now, it's time for nature to finally come around." Mewtwo calmly said with his strong voice as he released the bullets.

The bullets zoomed through the lab and flew down every hallway, killing every human in the lab. Corpses stated falling everywhere and what was supposed to be a time of celebration, ended up be the lab's doom. Mewtwo floated over to Mackey, who was barely hanging on to his life. Covered in blood, the scientist was on his last breaths before Mewtwo read his mind to find out how to release the captured Pokemon. After Mewtwo attained what he needed, he tossed Mackey into a wall, ending his life.

After finding the main board in the underground corridor, Mewtwo executed the coding combination needed to mass release the captured Pokemon. Nearly two hundred Pokemon including Ponyta, Absol, and Lopunny raced out of their cages. The corpses of their rulers being trampled over, they all climbed up the elevator shaft, ran out of the warehouse entrance, and dashed to a new life free of torture and experimentation.

Deoxys, laying on the floor and overcome with pain and confusion, watched as the Pokemon escaped. Mewtwo walked up to him and telepathically released Deoxys from the plasma wrap that was minimizing his power.

"Anti-Psychic cables. Main ingredient is the blood of Sharpedo. Hmm, interesting." Mewtwo remarked while freeing Deoxys.

"I don't get it, you're a psychic as well. You shouldn't even be able to control those cables telekinetically." Deoxys said, still in shock by what was transpiring.

"I can transform into a fighting half breed. Using that transformation, I trained myself to become resistant to certain dark type items and effects. But you and I have bigger problems." Mewtwo explained.

"Your other half is dead. The blue crystal Deoxys was killed by this lab's hunters using the technology attained by experimenting on dark types." Mewtwo said blankly

Deoxys had an expression of rejection. "No… no, you're lying! His body is designed for attack, there's no way he was murdered. He's more dangerous than me…"

"Which is exactly why they killed him. There was no way they could take him alive." Mewtwo interrupted.

The wave of truth and sadness overtook Deoxys. As his grief set in the only words he could say were "Why are you doing any of this?"

Mewtwo answered. "I need your help Deoxys. Me and you are going to kill Arceus."

 **TO BE CONTINUED…**


	2. Whirlpools

**CHAPTER 2 – WHIRLPOOLS**

In the Western part of Johto, two figures flying over the sea come to a halt. The harsh winds and seemingly endless whirlpools blocking the way will not let them advance any further.

"Darkai, we're not getting through here. We'll be blown into the whirlpools and sucked into the bottom of the sea instantly," said Genesect.

Darkrai closed his eyes and concentrated his energy. "Wait," he commanded.

Darkrai raised his hands and shouted, "Ominous wind!" The clouds above became darker and a strong gust of wind came down on the sea ahead. Soon the whirlpools started to thin out and become shallow until the sea was calmed, and the whirlpools were no more. The intense wall of wind dissipated and a path to island ahead was cleared.

"Well... that's one way to do it," acknowledged Genesect. Darkrai released his powerful force and opened his eyes. "Let's move," he demanded.

Darkrai and Genesect flew swiftly over the rest of the sea and arrived at Whirl Islands. Landing on the beach, Genesect took a second to inspect the area. The beach was populated by Krabbys and entrances to multiple caves.

"There's no sign of them around. How long do you think it will take to find them?" Genesect asked in his robotic voice.

"They've found us. Look up," Darkrai declared.

On the peaks of the mountain top above, there were three bird-like shapes that were staring directly at the duo. As Genesect looked closer, they started to look more familiar until they were finally recognizable. It was Moltres on the left, Zapdos on the right, and Articuno in the middle. The legendary birds were alerted on their arrival.

"There goes the element of stealth." Genesect quipped. "What's the plan Darkrai?"

"Let me deal with Moltres, you won't be able to take its attacks. And remember, we need them alive for this to work." Darkrai ordered. Genesect nodded and concentrated his aim on Articuno and Zapdos.

The peak of the left perch crumbled as Moltres charged towards Genesect with flame charge. Darkrai intercepted Moltres with a quick attack which flinched Moltres, and then a dark pulse which sent the flaming bird flying into a cave below. As Darkrai followed Moltres into the collapsing cave, Genesect flew high into the sky as the clouds began to darken once more. Zapdos started generating powerful lightning strikes from the clouds to damage Genesect, who was narrowly dodging the strikes flying at rapid speeds and weaving through mountains. Articuno appeared behind Genesect and fired an ice beam. The ice beam coated half of Genesect's backside with a layer of ice, stunting his flight and sending Genesect into a free fall.

"Damn it, I'm frozen," Genesect shouted as he started falling towards the sea. He used his metal claw to start chipping away at the ice as Zapdos was prepared to fire another lightning strike. In the nick of time, Genesect chipped off the ice that was covering his boosters and charged back into flight, narrowly avoiding another bolt of lightning.

"Alright, let's try this," Genesect said to himself as he activated double-team. Genesect then seemingly started to multiply. Two became four, four became eight, eight became sixteen. In a couple seconds there one hundred and twenty-eight Genesects headed for Articuno. As Articuno flew away in opposite direction, Zapdos was rapidly destroying the illusions with lightning strikes. Articuno looked back and started firing ice beams at the illusions, destroying even more of them. Just as Articuno turned its head back around, it felt something in its chest and instantly stopped. It was almost as if it was a steel beam that stabbed into its body.

It was the real Genesect, impaling Articuno with it's metal arm.

"Gotcha," Genesect cheered. He then started striking Articuno with numerous metal punches before throwing it to the beach below. Articuno was finished.

Genesect and Zapdos started hearing rocks and boulders rumbling from the cave on the other side of the beach. Blasting out of the collapsed cave was Darkrai, holding Moltres by it's neck. Darkrai tossed Moltres aside and concentrated his attention on Zapdos.

"One more" Darkrai exclaimed. Zapdos, enraged by the sight of its fallen allies, left its perch and directed all of it's power in the clouds above. The skies went from a dark gray to a jet black, and lightning strikes powerful enough to completely combust the trees below began to rain down onto the island.

"Genesect, keep using double team, don't get hit. On my command, fire at Zapdos," Darkrai instructed. As soon as Darkrai gave his order, he sunk into the beach and became a silhouette of himself, in the form of a shadow. The shadow moved into the forest and disappeared.

"Don't get hit. Great advice," Genesect retorted as he started making more illusions.

Darkrai, as a shadow, zoomed past the forest and reached the edge of the mountain. The shadow started climbing up the mountain, getting closer and closer to the height that Zapdos was flying at. Zapdos was concentrated on Genesect and taking out his illusions at a much faster rate than Genesect could generate them. Genesect was soon down to three copies. As lightning strikes quickly destroyed the last two illusions and only the real Genesect remained, Darkrai jumped out of the shadow which was now at the peak of the mountain and appeared behind Zapdos.

"Genesect now!" Darkrai shouted. Darkrai launched a dark pulse at Zapdos which sent it flying towards the beach with the weight of the force. Genesect launched a flash cannon from the gun on its back towards Zapdos, and then Zapdos found itself being crushed between the forces of the flash cannon and the dark pulse. The reaction between the two attacks exploded, and Zapdos was sent spiraling into the forest below. The intense lightning from the clouds above stopped and Darkrai floated down to the ground.

Genesect grabbed Moltres and dragged it over to the incapacitated Articuno. Darkrai floated out of the forest with Zapdos, beaten and hardly breathing, telekinetically floating next him. He threw Zapdos down next to it's allies.

"That's it huh? This will bring out the big bird?" Genesect inclined.

Darkrai did not answer him. Instead, he stepped on Zapdos's neck prompting it to screech loudly. Then, from under the sea, there was a roar that shook the whole island.

* * *

In the heart of the Sinnoh region, Mewtwo and Deoxys trek down a hidden crypt, not marked on any map or recognized by human technology. Mewtwo leads the way down the crypt with a knapsack on his back and a torch floating beside him. Deoxys cautiously follows behind, not knowing exactly what he's getting into. They soon come to a stop, as there is a large boulder blocking the way.

"Dead end," Deoxys muttered. Mewtwo raised his hand and lifted the boulder out of the way and to the side. "Not exactly," Mewtwo responded.

The two legendary pokemon walked through the entrance. They came to a wall with two long candles to the side of it. Mewtwo lit up the candles with is torch and brightened the cavern, which revealed hieroglyphics on the wall.

"Ancient writing," Deoxys observed, as he started translating the wall.

 _KEY TO THE CRADLE:_

 _PIERCE THE STORM (LUGIA)_

 _PIERCE THE SKY (RAYQUAZA)_

 _PIERCE THE MATTER (GIRATINA)_

 _PIERCE THE AURA (ZYGARDE)_

 _PIERCE THE LIMIT (KYUREM)_

"Mewtwo, what is this?" Deoxys inquired.

"This is the key to the cradle. Five different keys hidden inside the minds of five legendary pokemon. Once all five keys are collected, access is granted to Arceus's private dimension where he sleeps undisturbed for thousands of years," Mewtwo explained, as turned to face Deoxys.

"Darkrai is plotting to collect all the keys and enter the cradle. He will then trap Arceus in an eternal nightmare and take over his body" Mewtwo insisted.

"Darkai will become a god." Deoxys reflected. Mewtwo nodded "Yes, exactly. We need to collect all five keys before Darkrai does. I can shut down Arceus's mind down while he's sleeping and kill him."

Deoxys was wrapping the situation around his head. "Wait, why do we have to kill Arceus? Why don't we just stop Darkai, or wake him up?"

"And then what? Arceus still exists with the power to destroy everything as we know it. Do you really want to risk waking Arceus up so he can put the world in peril again? Even putting a stop to Darkrai is a long shot. Palkia and Dialgia hit Darkrai so hard that he was warped out of the fabric of space-time, and he came back more powerful than ever," Mewtwo sneered. "Arceus has put the world in danger more times than he's tried to help it, even if he created the universe. The only way to make sure a bomb doesn't detonate is to diffuse it for good."

Deoxys sighed. "Okay, I understand what you're saying, but why do you need me?"

Mewtwo explained himself. "You're the only telepath on my level that I can trust with a mission like this. The only way to get these keys is to tire the keyholders out in battle and enter their minds, assuming they don't want to give them up willingly or they're not sleeping. I can't do this alone. Also…" Mewtwo opened his knapsack and pulled out a grayish gem that was in the core of the dead Deoxys.

Deoxys in shock looked at the gem and instantly recognized it. "That jewel, that's…"

"Yes", Mewtwo interrupted. "The gym to the other Deoxys. I know how you work. If the gym is intact you can regenerate, right? Arceus's dimension is filled with life energy, generated by the Jewel of Life itself. If we get this gem inside the cradle, your friend will come back to life. So, do we have a deal?"

Deoxys took a second to contemplate the decision. But the thought of reviving his counterpart left him no choice. Finally, Deoxys responded. "Okay, I'm in. But why would Darkrai be doing this? As evil as he looks, he's not that way."

Mewtwo put the gem back inside his knapsack. "There's a lot more to explain, but we have to get started immediately. Come on, we have find Lugia before Darkrai does."

 **TO BE CONTINUED…**


End file.
